Why won't our Macbook shut down?

Check the console logs ( /Applications / Utilities / Console.app ).

First close all your applications. Then make a note of the time on the clock and then shut down.  When you restart Open Console and copy and paste the console logs from the time you started to shut down until you began to restart here.

You could also type command-option-escape when the computer refuses to shut down. This may bring up the force-quit dialogue and tell you what process or application has not quit.

Here is the last few things in the log before it froze (notice the last entry is several hours later).  Looks like LogMeIn is the last thing in the log.  That software is used regularly though and is up to date.  Thoughts?

2/15/12 4:43:36 PM      com.logmein.logmeinguiagent[137]      Session - Error occured:read errno: (9) Bad file descriptor
2/15/12 4:43:36 PM      com.logmein.logmeinguiagent[137]      2012-02-15 16:43:36.201 - Debug     - LMIGUIAgent - SessionManager - Connection closed
2/15/12 4:43:36 PM      com.logmein.logmeinguiagent[137]      2012-02-15 16:43:36.317 - Debug     - LMIGUIAgent - SessionManager - Closing DisplayServer
2/15/12 4:43:36 PM      com.logmein.logmeinguiagent[137]      2012-02-15 16:43:36.317 - Debug     - LMIGUIAgent - SessionManager - DisplayServer close
2/15/12 4:43:36 PM      com.logmein.logmeinguiagent[137]      2012-02-15 16:43:36.318 - Debug     - LMIGUIAgent - SessionManager - Exiting
2/15/12 4:43:36 PM      com.apple.launchd[1]      (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems": No such file or directory
2/15/12 4:43:36 PM      com.apple.launchd[1]      (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems": No such file or directory
2/15/12 4:43:36 PM      com.apple.launchd[1]      (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems": No such file or directory
2/15/12 4:43:36 PM      com.apple.launchd[1]      (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems": No such file or directory
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      cfg: cannot open [/Users/Yvonne/Library/Application Support/LogMeIn Hamachi/h2-ui-override.cfg]
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      ipc: connected to /Library/Application Support/LogMeIn Hamachi/run/ipc.sock
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      gui_link: connected to /Library/Application Support/LogMeIn Hamachi/run/ipc_gui_link_4292568.sock
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      gui_link: 6 listening at /Library/Application Support/LogMeIn Hamachi/run/ipc_gui_link_4292568.sock
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      tcp: laggy read, breaking out..
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      mbapp: message queue became empty
2/15/12 4:43:36 PM      com.logmein.hamachimb[139]      tcp: laggy read, breaking out..
2/15/12 4:43:37 PM      com.apple.launchd.peruser.503[116]      (com.logmein.logmeinguiagent[137]) Exited with exit code: 1
2/15/12 7:38:06 PM      com.apple.launchd[1]      *** launchd[1] has started up. ***

Certainly does look like Logmein is the culprit. You could try force quitting it (Command-option-excape), then see if the computer will shut down normally. If it does, then you know the trouble is logmein and we can work from there.

Thanks.  We had tried manually closing LogMeIn before shutting down and it did shutdown okay.  However, a quick test with it enabled did the same thing.  It's hard to tell because although it's been occurring more frequently, it doesn't happen every time.  When it does happen though, you can't force quit, you can't do anything to interact with the GUI at all and are forced to power off.  

Just for test purposes we have removed LogMeIn from the machine and will give it a couple days and see if the problem is gone for good.  If it is, we can try reinstalling LogMein and see if that starts the problem again.

It froze again during shutdown. :(  this is with all LogMeIn stuff removed.

Repairing permissions now.

We did notice a lot of these entries in the console log. Any concern there?

2/15/12 4:43:36 PM      com.apple.launchd[1]      (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems": No such file or directory

Here are instructions on how to get rid of that message. You might try it and see if that helps:

http://forums.macrumors.com/showthread.php?t=1192157

You could also try downloading and installing Combo Update 10.6.8 v. 1.1

Notwithstanding that you are already at 10.6.8, the combo update sometimes fixes things that fell through the cracks with incremental updates.

Still trying to repair permissions. It's been saying 31 minuts remaining for quite a while. Machine is still responsive though. Possible for it to take that long?

It can take awhile.

Once it is done, while you have Disk Utllity open, also run Verify Disk and make a note of the S.M.A.R.T. status of your drive.

Thanks. Just finished. Running veryify disk now. Typically how long does that take?  120gb white MacBook

I would guess 10 minutes or so.

Did you happen to notice what the S.M.A.R.T. status was?  The S.M.A.R..T. status shows up at the bottom right of the Disk Utility window when you click on the hard drive (not the volume) at the upper left. See attached screenshot.
Screen-Shot-2012-02-15-at-9.10.3.pdf

Verify says the volume is okay. Will go back and check smart status now.

Found this post on an Apple board for a similar problem
"Remove everything from Accounts > Login Items and (even more important) from /Library/StartupItems as well as /Library/LaunchAgents and LaunchDaemons"

We have nothing in startup items. In launchdaemons we have the following:
Com.google.third-party-32b-kext-logger.plist
Com.google.keystone.daemon.plist

Under launch agents we have:
Com.google.keystone.agent.plist

Are those of concern?

In login items we just have some network drives and Dropbox, been there forever.

Deleting the plist files won't hurt, If needed they will be automatically regenerated.

Ok. Smart status is verified

Trying the safe boot now then we will be out of things to try:
"Safe Boot by holding Shift key on restart. No need to log in, just restart from log in screen."

So anotherwords boot into safe boot but don't actually do anything there, then just restart regularly?  What is the purpose of that?

Thanks

Starting in safe boot mode runs some disk routines that can't be run unless you started off of another disk. It also wipes out the boot cache.

Thanks everyone.  Split the points up to both of you as it's hard to tell which of the solutions finally stopped the problem.  Seems like it's fixed now!  Has not occurred again!